BLAST using Biopython

Question

[a.lathifbt]

Hello.I am new to biopython and I am trying to do BLAST search for a single query sequence. This is the script I wrote:

""" BLAST OVER INTERNET """
from Bio.Blast import NCBIWWW
file_name=input("enter the file name:")
filename = open(file_name).read()
result=NCBIWWW.qblast("blastn", "nt", "filename")
from Bio.Blast import NCBIXML
blast_record = NCBIXML.read(result)
print(len(blast_record.alignments))
evalue = 0.01
for alignment in blast_record.alignments:
   for hsp in alignment.hsps:
     if hsp.expect < evalue:
       print("****Alignment****")
       print("sequence:", alignment.title)
       print("length:", alignment.length)
       print("e value:", hsp.expect)
       print(hsp.query[0:75] + "...")
       print(hsp.match[0:75] + "...")
       print(hsp.sbjct[0:75] + "...")

So the issue I am getting is, no result is being generated. The length of the "blast_record_allignments" returns 0 value. Can anyone please help me with it? Thanks in advance

[Sej Modha]

Please use 101010 button to format the code. Could you provide a samples fasta sequence you're using for this script?

Answer 1

[massa.kassa.sc3na]

few problems: You pass the STRING "filename" to the NCBIWWW.qblast call instead of variable.

If the file from input should be FASTA file, then you need to pass file_name variable (without quotes) and the open(..).read() is not necessary.

[a.lathifbt]

Thank you so much! rectified the issue and it's working now.

[Joe]

Great. I’ve moved the comment to an answer, so if you’re happy with the resolution to the thread, please go ahead and toggle the Tick to accept the answer as a solution.